tbuckley/cabot-search huggingface dataset:
Abstract IA006: Immunobiology of sarcomas and therapeutic implications
Authors: Nicolas J. Llosa
Journal: Clinical Cancer Research (2022)

Abstract Undoubtedly, the greatest breakthrough in cancer treatment over the past decade has been immunotherapy. However, the immunosuppressive nature of the tumor microenvironment (TME) remains the biggest obstacle to increasing the number of patients that respond to immunotherapy. Unfortunately, initial trials of immune checkpoint inhibitors in patients with soft tissue sarcoma (STS) have achieved very limited success, and the reasons for this are crudely unappreciated. Hence, it is critical to move beyond the current focus on targeting individual cell types of interest and rather adopt a more comprehensive systems-level approach in which we analyze and integrate all the TME components to identify and disable the critical nodes. Our team has characterized the immunobiology of STS via cutting–edge high-dimensional mapping platforms that we have established and standardized for analyzing specimens from patients with STS. We have discovered that tumor infiltrating myeloid cells (TIM) penetrate and dominate the TME of STS provoking the suppression of effective antitumoral T cell immune responses. Using a set of sophisticated multiscale techniques, we deconvoluted the TME of various STS creating a comprehensive map of all immune cell populations present and dissected out chemokine gradients of specific histological regions relevant for the recruitment and development of TIM in the TME of STS. STS TIM are regulated by tumor-derived cytokines to acquire a polarized immunosuppressive phenotype, which in turn de-activates the T cell compartment in the TME. In this way, we elucidated unique myeloid populations as key facilitators of STS progression and mediators of local tumor immunosuppression. Furthermore, we defined metabolic pathways utilized by TIM that contribute to their immunosuppressive properties in STS and manipulated them via glutamine antagonism in our mouse model of STS. Our intervention generated a TME that was less acidic, less hypoxic and more replete with nutrients leading to an intratumoral influx of T cells, both CD4+ and CD8+ cells, along with B cells. These modifications in the TME in combination with anti PD-1 therapy induced better endogenous anti-tumor responses and repurposed TIM markedly thereby reducing the tumor size and improving the survival of mice. Thus, we propose a metabolic strategy to therapeutically target the TME of STS and reprogram their immunosuppressive myeloid niche as a means of enhancing immunotherapy. Citation Format: Nicolas J. Llosa. Immunobiology of sarcomas and therapeutic implications [abstract]. In: Proceedings of the AACR Special Conference: Sarcomas; 2022 May 9-12; Montreal, QC, Canada. Philadelphia (PA): AACR; Clin Cancer Res 2022;28(18_Suppl):Abstract nr IA006.
Abstract PR007: A single cysteine in PAX3-FOXO1 is relevant for transactivation and survival of rhabdomyosarcoma cells
Authors: Beat W. Schäfer, Katharina Benischke, Jakob Wurth, Dominik Laubscher, Quy A. Ngo, Sara Danielli, Marco Wachtel
Journal: Clinical Cancer Research (2022)

Abstract The fusion transcription factor PAX3-FOXO1 (P3F) is the major driver of alveolar rhabdomyosarcoma. Since these tumors are characterized by a mostly quiet mutational landscape and a paucity of druggable oncogenes, the fusion protein itself remains the most important drug target. Transcription factors are challenging proteins for drug development since they lack enzymatic activities and are, apart from DNA binding domains, largely intrinsically disordered. Identification of defined and possibly druggable structures in such proteins is therefore of great clinical interest. Towards this aim, we performed a CRISPR/Cas9-based domain screen in P3F-positive rhabdomyosarcoma cells and identified a small, structured and highly important domain within the transactivation domain of P3F. Further, we demonstrate that cysteine C793 located in this region is indispensable for target gene activation by P3F. Its mutation significantly reduced cell proliferation and induced differentiation of RMS cells. Mechanistically, we identified p300/CBP proteins as important co-factors and interactors of C793 that co-regulate a majority of P3F target genes. Their inhibition/degradation by small molecules efficiently reduces rhabdomyosarcoma cell survival. These data suggest that mainly one single amino acid drives oncogenicity of P3F and identify a potentially targetable structure within the fusion protein. Citation Format: Beat W. Schäfer, Katharina Benischke, Jakob Wurth, Dominik Laubscher, Quy A. Ngo, Sara Danielli, Marco Wachtel. A single cysteine in PAX3-FOXO1 is relevant for transactivation and survival of rhabdomyosarcoma cells [abstract]. In: Proceedings of the AACR Special Conference: Sarcomas; 2022 May 9-12; Montreal, QC, Canada. Philadelphia (PA): AACR; Clin Cancer Res 2022;28(18_Suppl):Abstract nr PR007.
Abstract B004: ATR-CHK1-WEE1 pathway is a critical dependency in the context of DNA damage and replicative stress in osteosarcoma
Authors: Leanne C. Sayles, Henry Martell, Amanda Koehne, Kean-Hooi Ang, Chris Wilson, Michelle Arkin, E. Alejandro Sweet-Cordero
Journal: Clinical Cancer Research (2022)

Abstract Osteosarcoma (OS) is characterized by widespread somatic copy number alterations (SCNAs) and structural variations (SVs) with few recurrent point mutations. We previously demonstrated proof-of-principle for a genome-informed strategy for treatment of OS based on rank-ordering SCNAs within specific oncogenes identified by WGS and RNAseq. Although we identified several potentially effective therapeutic strategies using this approach, it is likely that effective therapy for OS will require use of combination therapies. To identify new combination therapy approaches for OS, we used a panel of PDX-derived cell lines (PDXC) and performed a combination drug screen. We assessed 5 drug backbones against 15 targeted agents in 8 PDXC and 2 established OS cell lines. When we combined Gemcitabine with agents that target the ATR-CHK1-WEE1 pathway, we observed strong synergy across all PDXC tested. These results were validated in a secondary screen using a combination matrix across 10 PDXC. Use of targeted agents inhibiting ATR, CHK1 or WEE1 in combination with Gemcitabine led to decreased proliferation and a marked increase in apoptosis in vitro. In subcutaneous tumor models, we observed that decreased tumor growth with either ATRi or Gemcitabine alone, whereas tumors shrank when treated with the combination. However, when we treated OS774 in vivo, there was no effect on tumor growth for either single agent alone or when in combination. This effect was dependent on the presence of ATR as a PDXC with no ATR detectable by western blotting showed not effect in vivo. In an orthotopic model in which PDXC are implanted along the tibia, this combination therapy effectively decreased tumor growth. In a lung metastasis model, ATRi and Gemcitabine resulted a durable reduction in metastatic lesions over time. In summary, we have identified a susceptibility to the ATR-CHK1-WEE1 pathway when combined with gemcitabine. These studies suggest that further investigation ATR-CHK1-WEE1 and gemcitabine are warranted to address the unmet need for new therapeutic approaches for relapsed and recurrent OS patients. Citation Format: Leanne C. Sayles, Henry Martell, Amanda Koehne, Kean-Hooi Ang, Chris Wilson, Michelle Arkin, E. Alejandro Sweet-Cordero. ATR-CHK1-WEE1 pathway is a critical dependency in the context of DNA damage and replicative stress in osteosarcoma [abstract]. In: Proceedings of the AACR Special Conference: Sarcomas; 2022 May 9-12; Montreal, QC, Canada. Philadelphia (PA): AACR; Clin Cancer Res 2022;28(18_Suppl):Abstract nr B004.
Abstract PR004: Fusion protein-driven IGF-IR signals deregulate hippo pathway promoting oncogenic cooperation of YAP1 and FUS-DDIT3
Authors: Ruth Berthold, Ilka Isfort, Cihan Erkut, Lorena Heinst, Inga Grünewald, Eva Wardelmann, Thomas Kindler, Pierre Åman, Thomas G.P. Grünewald, Florencia Cidre-Aranaz, Marcel Trautmann, Stefan Fröhling, Claudia Scholl, Wolfgang Hartmann
Journal: Clinical Cancer Research (2022)

Abstract Introduction: Myxoid liposarcoma (MLS) is molecularly characterized by a recurrent chromosomal translocation which generates a chimeric FUS-DDIT3 fusion gene. The FUS-DDIT3 oncoprotein, acting as a transcriptional dysregulator, has been shown to be essential in MLS pathogenesis, among others through deregulation of IGF-IR/PI3K/AKT signaling, but its exact mode of function remains incompletely understood. Recently, a particular reliance on the Hippo pathway effector and transcriptional co-regulator YAP1 was found in MLS; however, the molecular mechanism of FUS-DDIT3-dependent YAP1 activation and its contribution to MLS pathogenesis remain unclear. Experimental Procedures: The expression of IGF-IR and YAP1 was analyzed in a large cohort of MLS specimens by immunohistochemistry. In vitro analyses were performed employing a human mesenchymal stem cell system stably expressing FUS-DDIT3 and human MLS cell lines. RNA interference-based approaches, experiments with small-molecule kinase inhibitors, co-immunoprecipitation, proximity ligation assays, transcriptome sequencing and adipogenic differentiation assays were performed to determine the interplay of FUS-DDIT3, IGF-IR-dependent signals, and YAP1 in MLS cells. Results: Immunohistochemically, a significant subset of MLS samples showed concurrent expression of IGF-IR and nuclear YAP1. In vitro, FUS-DDIT3-driven IGF-IR signaling was found to promote stability and nuclear accumulation of YAP1 via deregulation of the Hippo pathway. Co-immunoprecipitation and proximity ligation assays revealed nuclear co-localization of FUS-DDIT3 and YAP1 in FUS-DDIT3-expressing mesenchymal stem cells and MLS cell lines. Transcriptome sequencing of MLS cells demonstrated that FUS-DDIT3 and YAP1 co-regulate specific oncogenic gene signatures related to proliferation, cell cycle progression, apoptosis, and adipogenesis. In differentiation assays, FUS-DDIT3 and YAP1 were found to cooperate in adipogenic differentiation arrest. Conclusions: Our study provides molecular insights into a complex FUS-DDIT3-driven network involving IGF-IR signals acting on Hippo/YAP1, and uncovers cooperative effects of YAP1 and FUS-DDIT3 in the pathogenesis of MLS. Citation Format: Ruth Berthold, Ilka Isfort, Cihan Erkut, Lorena Heinst, Inga Grünewald, Eva Wardelmann, Thomas Kindler, Pierre Åman, Thomas G.P. Grünewald, Florencia Cidre-Aranaz, Marcel Trautmann, Stefan Fröhling, Claudia Scholl, Wolfgang Hartmann. Fusion protein-driven IGF-IR signals deregulate hippo pathway promoting oncogenic cooperation of YAP1 and FUS-DDIT3 [abstract]. In: Proceedings of the AACR Special Conference: Sarcomas; 2022 May 9-12; Montreal, QC, Canada. Philadelphia (PA): AACR; Clin Cancer Res 2022;28(18_Suppl):Abstract nr PR004.
Abstract IA014: Stem cell and developmental hierarchies in rhabdomyosarcoma
Authors: David M. Langenau, Yun Wei, Qian Qin, Luca Pinello
Journal: Clinical Cancer Research (2022)

Abstract Rhabdomyosarcoma (RMS) is the most common soft-tissue sarcoma of childhood and is comprised of at least two major molecular subtypes. Despite sharing features with skeletal muscle, the conservation of underlying cellular hierarchy with human muscle development and the identification of molecularly-defined tumor-propagating cells have not been reported. Using single-cell RNA sequencing of patient-derived RMS, DNA-barcode cell fate mapping, antibody enrichment and functional stem cell assays, and mouse xenograft modeling, we have uncovered tumor cell hierarchies in Fusion-negative (FN-) RMS that are shared with normal human muscle development. We also identified common developmental stages at which tumor cells become arrested. FN-RMS resemble early muscle found in embryonic and larval development, while fusion-positive (FP-) RMS express a highly specific developmental gene program found in muscle cells transiting from embryonic to fetal development at 7-7.75 weeks of age. FP-RMS also have neural-pathway enriched cell states, suggesting less-rigid adherence to muscle development hierarchies in this disease. Finally, we identify a new molecularly-defined tumor-propagating cell in FN-RMS that shares remarkable similarity to the newly described bi-potent, muscle mesenchyme stem/progenitor cell that makes both muscle and osteogenic cells. Citation Format: David M. Langenau, Yun Wei, Qian Qin, Luca Pinello. Stem cell and developmental hierarchies in rhabdomyosarcoma [abstract]. In: Proceedings of the AACR Special Conference: Sarcomas; 2022 May 9-12; Montreal, QC, Canada. Philadelphia (PA): AACR; Clin Cancer Res 2022;28(18_Suppl):Abstract nr IA014.
Abstract A018: YAP signaling promotes resistance to MEK and AKT inhibition in NF1-related MPNSTs
Authors: Lauren McGee, Curt Essenburg, Lisa Turner, Angela Hirbe, Anwesha Dey, Jason Zbieg, Carrie Graveel, Matt Steensma
Journal: Clinical Cancer Research (2022)

Abstract Malignant peripheral nerve sheath tumors (MPNSTs) are a rare and deadly sarcoma with few therapeutic options that are the leading cause of death for patients with Neurofibromatosis Type 1 (NF1). MPNSTs are characterized by a large burden of genomic alterations, chemoresistance, and a 5-year survival rate of 25-50%. NF1 is the major negative regulator of RAS, therefore a hallmark of MPNSTs is deregulated RAS/MAPK signaling. To date, no targeted therapies have been approved for MPNST treatment, highlighting the need for an understanding of adaptive signaling mechanisms that drive resistance. The HIPPO pathway is a key regulator of organ growth and cellular differentiation and is a central driver of resistance to RAS pathway inhibition in other cancers. The key HIPPO effector, YAP1, interacts with RAS and AKT signaling pathways, creating alternate routes for resistance in multiple cancers. In our studies, we identified strong YAP activation in response to MEK and AKT inhibition in MPNST cell lines. Since YAP acts as a transcriptional co-activator through interaction with TEAD transcription factors, we proposed that targeting the Hippo pathway in MPNST will abrogate MAPK inhibitor resistance. To investigate tumor signaling responses and efficacy in vivo, we utilized 3 genomically distinct MPNST patient-derived xenograft (PDX) models. To assess drivers of MPNST resistance, we have developed a preclinical model of drug resistance that simulates clinical treatment schedules. Using a cross-over and a drug holiday design, we are able to evaluate patterns of response and resistance to resumed treatment. We observed distinctive responses to MEK and AKT inhibitors in each PDX line; however, the impact on MPNST growth was minimal with single agent treatment. Comparison of pathway activation between the “drug holiday” biopsies and the treatment endpoint, demonstrated distinct YAP and RAS (pERK) activation levels in resistant tumors. For example, strong YAP activation is observed in correlation with decreased pERK in resistant tumors. YAP activation was strongest at the invasive edge of viable tumor regions. Currently, we are evaluating the efficacy and signaling adaptations to investigate the underlying molecular mechanisms in these MPNST models. Overall, we have demonstrated the development of a clinically relevant model of MPNST resistance and a potential switch between RAS and YAP signaling that promotes resistance to MEK or AKT inhibition. Citation Format: Lauren McGee, Curt Essenburg, Lisa Turner, Angela Hirbe, Anwesha Dey, Jason Zbieg, Carrie Graveel, Matt Steensma. YAP signaling promotes resistance to MEK and AKT inhibition in NF1-related MPNSTs [abstract]. In: Proceedings of the AACR Special Conference: Sarcomas; 2022 May 9-12; Montreal, QC, Canada. Philadelphia (PA): AACR; Clin Cancer Res 2022;28(18_Suppl):Abstract nr A018.
Abstract IA009: Oncogenic transcription factors drive highly tumor-specific LincRNA
Authors: Olivier Delattre, Julien Vibert, Olivier Saulnier, Joshua Waterfall
Journal: Clinical Cancer Research (2022)

Abstract Many cancers are characterized by gene fusions encoding oncogenic chimeric transcription factors (TFs) such as EWS::FLI1 in Ewing sarcoma (EwS). EWS::FLI1 induces a complete reprogramming of mesenchymal stem cells, the putative cell of origin of Ewing sarcoma, through binding and subsequent generation of thousands of neoenhancers at GGAA microsatellite repeats. We show that EWS::FLI1 induces the robust expression of a specific set of novel spliced and polyadenylated transcripts within otherwise transcriptionally silent regions of the genome. These neo-genes (NGs) are virtually undetectable in large collections of normal tissues or non-EwS tumors and can be silenced by CRISPR interference at regulatory EWS::FLI1-bound microsatellites. Ribosome profiling and proteomics further show that some NGs are translated into highly EwS-specific peptides. More generally, hundreds of NGs can be detected in diverse cancers characterized by chimeric TFs. Altogether, we identify the transcription, processing, and translation of novel, specific, highly expressed multi-exonic transcripts from otherwise silent regions of the genome as a new activity of aberrant TFs in cancer. These neotranscripts, which can be classified as LincRNAs, or neopeptides may have specific functions in the tumor cells. The latter may also constitute ideal neoepitopes as they are tumor-specific, clonally expressed in sarcoma cells, induced by the driver genetic alterations and public for a given sarcoma. Citation Format: Olivier Delattre, Julien Vibert, Olivier Saulnier, Joshua Waterfall. Oncogenic transcription factors drive highly tumor-specific LincRNA [abstract]. In: Proceedings of the AACR Special Conference: Sarcomas; 2022 May 9-12; Montreal, QC, Canada. Philadelphia (PA): AACR; Clin Cancer Res 2022;28(18_Suppl):Abstract nr IA009.
Abstract IA019: How to target lung metastasis: dynamic changes in chromatin accessibility during osteosarcoma lung metastasis expose vulnerabilities
Authors: Peter C. Scacheri
Journal: Clinical Cancer Research (2022)

Abstract The metastatic cascade describes the series of steps required for a cancer cell to successfully spread from its primary tumor to a secondary organ. Despite knowing that metastasis is a fluid process, almost all studies to date have relied on end-point assays. As a result, little is known about the continuum of molecular events required for successful growth within the secondary organ. By profiling accessible chromatin in osteosarcoma cells grown in vitro and isolated from an early and late timepoint during lung metastasis, we identify temporally distinct epigenomic reprogramming events that occur as tumors form and grow within the metastatic microenvironment. Furthermore, these data pinpoint key upstream transcription factors responsible for the dynamic chromatin changes. Through paired in vivo and in vitro CRISPR drop-out screens, we show a subset of these putative pro-metastatic transcription factors are essential for lung metastasis, but dispensable for in vitro growth. Targeting the same factors with chemical probes in vitro and ex vivo demonstrated similar context-dependent essentiality. Altogether, our study demonstrates the epigenomes of metastasizing cancer cells are tightly regulated in a dynamic and context-specific manner, and the transcription factors controlling this process may serve as novel vulnerabilities. Citation Format: Peter C. Scacheri. How to target lung metastasis: dynamic changes in chromatin accessibility during osteosarcoma lung metastasis expose vulnerabilities [abstract]. In: Proceedings of the AACR Special Conference: Sarcomas; 2022 May 9-12; Montreal, QC, Canada. Philadelphia (PA): AACR; Clin Cancer Res 2022;28(18_Suppl):Abstract nr IA019.
Abstract IA010: Novel targeted therapy approaches in NF1-MPNST
Authors: Christine A. Pratilas
Journal: Clinical Cancer Research (2022)

Abstract NF1 is an essential negative regulator of RAS activity and its function is lost in nearly 90% of malignant peripheral nerve sheath tumors (MPNST). Additional recurrent molecular changes include loss of function alterations in CDKN2A, TP53, EED and SUZ12, but molecular targeting of these genomic events represents a unique challenge. We previously reported that the efficacy of MEK inhibitor is limited by adaptive activation of receptor tyrosine kinases and the adaptor protein SHP2, and that combined inhibition of MEK and SHP2 is effective in MPNST. However, the clinical potential of combination MEK and SHP2 inhibitors may be limited by the overlapping toxicity induced by ERK pathway inhibition. Genetic depletion of PTPN11 has substantial growth inhibitory effects in preclinical models of MPNST, suggesting that SHP2 is an exciting new focus for targeted therapy development in NF1-MPSNT. Loss of CDKN2A, inactivation of RB1, and hyperactivation of cyclin dependent kinases (CDK) in MPNST also suggest that small-molecule CDK4/6 inhibitors (CDK4/6i) may offer a potential combination strategy. Our preclinical data suggest that this combination is active, well-tolerated, and has the potential for immediate advancement into clinical trials. Citation Format: Christine A. Pratilas. Novel targeted therapy approaches in NF1-MPNST [abstract]. In: Proceedings of the AACR Special Conference: Sarcomas; 2022 May 9-12; Montreal, QC, Canada. Philadelphia (PA): AACR; Clin Cancer Res 2022;28(18_Suppl):Abstract nr IA010.